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Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement

Plant Phenomics 2020年第1期2卷 118-121页

作者： Ian R.Braun Colleen F.Yanarella carolyn j.lawrence-dill Interdepartmental Bioinformatics and Computational Biology Iowa State UniversityAmesIA 50011USA Department of Genetics Development and Cell BiologyIowa State UniversityAmesIA 50011USA Department of Agronomy Iowa State UniversityAmesIA 50011USA

Many newly observed phenotypes are first described,then experimentally manipulated.These language-based descriptions appear in both the literature and in community datastores.To standardize phenotypic descriptions and enable simple data aggregation and analysis,controlled vocabularies and specific data architectures have been developed.Such simplified descriptions have several advantages over natural language:they can be rigorously defined for a particular context or problem,they can be assigned and interpreted programmatically,and they can be organized in a way that allows for semantic reasoning(inference of implicit facts).Because researchers generally report phenotypes in the literature using natural language,curators have been translating phenotypic descriptions into controlled vocabularies for decades to make the information computable.Unfortunately,this methodology is highly dependent on human curation,which does not scale to the scope of all publications available across all of plant biology.Simultaneously,researchers in other domains have been working to enable computation on natural language.This has resulted in new,automated methods for computing on language that are now available,with early analyses showing great promise.Natural language processing(NLP)coupled with machine learning(ML)allows for the use of unstructured language for direct analysis of phenotypic descriptions.Indeed,we have found that these automated methods can be used to create data structures that perform as well or better than those generated by human curators on tasks such as predicting gene function and biochemical pathway membership.Here,we describe current and ongoing efforts to provide tools for the plant phenomics community to explore novel predictions that can be generated using these techniques.We also describe how these methods could be used along with mobile speech-to-text tools to collect and analyze in-field spoken phenotypic descriptions for association genetics and breeding applications.

关键词： stores translating enable

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The evolution of copulation frequency and the mechanisms of reproduction in male Anolis lizards

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Current Zoology 2014年第6期60卷 768-777页

作者： Michele A. jOHNSON Mafia Veronica LOPEZ Tara K. WHITTLE Bonnie K. KIRCHER Alisa K. dill Divina VARGHESE juli WADE Trinity University Department of Biology One Trinity Place San Antonio Texas 78212 USA Michigan State University Departments of Psychology and Zoology East Lansing Michigan 48824 USA

The evolution of many morphological structures is associated with the behavioral context of their use, particularly for structures involved in copulation. Yet, few studies have considered evolutionary relationships among the integrated suite of structures associated with male reproduction. In this study, we examined nine species of lizards in the genusAnolisto determine whether larger copulatory morphologies and higher potential for copulatory muscle performance evolved in association with higher copulation rates. In 10–12 adult males of each species, we measured the size of the hemipenes and related muscles, the seminiferous tubules in the testes, and the renal sex segments in the kidneys, and we assessed the fiber type composition of the muscles associated with copulation. In a series of phylogenetically-informed analyses, we used field behavioral data to determine whether observed rates of copulation were associated with these morphologies.We found that species with larger hemipenes had larger fibers in the RPM (the retractor penis magnus, a muscle that controls hemipenis movement), and that the evolution of larger hemipenes and RPM fibers is associated with the evolution of higher rates of copulatory behavior. However, the sizes of the seminiferous tubules and renal sex segments, and the muscle fiber composition of the RPM, were not associated with copulation rates. Further, body size was not associated with the size of any of the reproductive structures investigated. The results of this study suggest that peripheral morphologies involved in the transfer of ejaculate may be more evolutionarily labile than internal structures involved in ejaculate production.

关键词：交配率演变蜥蜴形态结构机制雄性繁殖频率

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有限功能燃气涡轮发动机干润滑的可行性

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航空发动机参考资料 1990年第4期 43-61页

作者： dill.,j 徐以儒

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硬镀层轴承钢的滚动接触疲劳之评价

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摩擦学学报 1987年第1期 54-65页

作者： j.F.dill,M.N.Garbos,H.E.Hintermann,H.j.Boving,徐锦芬 AFWAL/POSL Wright-Patterson AFB OH Hughes Aircraft Company E1 Segundo CA LSRH Neuchatel Switzerland LSRH Neuchatel Switzerland

用常规的和新发展的抗滚动接触疲劳试验装置来确定不同类型的轴承钢上沉积几种硬质表面镀层的抗动态粘着和鳞剥(或称散裂),将化学气相沉积(CVD)、反应溅射(RS)、活性反应蒸镀和电镀的硬质镀层镀在常规的和粉末冶金工艺制成的作轴承滚动... 详细信息

用常规的和新发展的抗滚动接触疲劳试验装置来确定不同类型的轴承钢上沉积几种硬质表面镀层的抗动态粘着和鳞剥(或称散裂),将化学气相沉积(CVD)、反应溅射(RS)、活性反应蒸镀和电镀的硬质镀层镀在常规的和粉末冶金工艺制成的作轴承滚动元件的材料之滚动接触疲劳杆上。这个镀膜和测量计划的目的是为了阐明沉积类型和温度对不同钢底材的变形的影响,以及使用标准化的试验技术将滚动接触粘着定量化。数据表明,在镀层粘结力和变形趋向之间有很大的差别,两者都是随着镀层类型和沉积温度以及钢的显微结构而变化的。发现CVD CrC-TiC复合硬质镀层在赫芝负荷达4.83×10～9Pa(原文错为2.79Gpa——译者注)时显示出特别非凡的抗粘着和鳞剥。

关键词：滚动接触疲劳粘结性盘形 CVD TiC TiN 底材固体润滑轴承轴承钢

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搏杀本能——李小龙高徒眼中的截拳道

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拳击与格斗 2008年第9期 56-57页

作者：保罗 j·巴克斯约翰 T．·宾汉姆黄凯

格雷·地尔(GRAY dill)坦言自己之所以会受到武术的吸引就是想提高自卫能力。他对于亚洲武术的哲理与原则没有太多兴趣。他说:"我只想学习如何踢别人屁股"。"但是,当我年龄与智慧增长以后,才发现武术的哲理对于我的全面发展极为重要。现... 详细信息

格雷·地尔(GRAY dill)坦言自己之所以会受到武术的吸引就是想提高自卫能力。他对于亚洲武术的哲理与原则没有太多兴趣。他说:"我只想学习如何踢别人屁股"。"但是,当我年龄与智慧增长以后,才发现武术的哲理对于我的全面发展极为重要。现在,我每天都练习武术"阳"的一面(指实用技术——译者),同时也进行"阴"的一面的研究,比如发现内在能量与调息。我尽力在两者之间达到一种平衡。"当格雷·地尔1963年开始练习武术时,他选择的是空手道和柔术。直到三年以后,他才发现了截拳道。当时,他知道李小龙要出演"加藤"。"当我在

关键词：截拳道咏春拳李小龙

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口腔鳞癌细胞外泌体分离鉴定及基因表达谱研究

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中华肿瘤防治杂志 2018年第19期25卷 1343-1350页

作者：王世琴金佳佳胡慧珍孙贵军李志勇何祥一兰州大学口腔医学院甘肃兰州730000 中国农业科学院兰州兽医研究所甘肃兰州730000

目的口腔鳞状细胞癌（oral squamous cell carcinoma, OSCC）是口腔颌面部最常见的恶性肿瘤，易复发和转移，预后较差。寻找特异性的生物标志，进行无创性的早期筛查或诊断工具的开发，对改善OSCC患者预后差、生存率低、复发率高的现状... 详细信息

目的口腔鳞状细胞癌（oral squamous cell carcinoma, OSCC）是口腔颌面部最常见的恶性肿瘤，易复发和转移，预后较差。寻找特异性的生物标志，进行无创性的早期筛查或诊断工具的开发，对改善OSCC患者预后差、生存率低、复发率高的现状至关重要。本研究旨在对OSCC细胞（Cal27）及口腔上皮细胞（human oral epithelial cells, HOEC）来源的外泌体进行分离鉴定及基因表达谱分析，为寻找与OSCC相关的特异性外泌体提供研究基础。方法采用超速离心法从细胞培养上清中分离外泌体，透射电镜观察其形态特征，粒度仪分析其粒径，蛋白质印记法及流式细胞术检测其标志蛋白（ALIX、CD63、CD81）。利用高通量测序技术全面掌握两种外泌体基因表达谱，筛选差异表达基因，并进行生物通路分析。结果Cal27及HOEC外泌体均呈圆形或椭圆形，直径均分布在30～150dill，ALIX、CD63、CD81标志蛋白呈现阳性表达。基因表达谱分析结果显示，两种外泌体间发生差异有统计学意义，｜log2Fold Changel〉｜，q〈0．001。表达变化的基因共有336个，KEGG生物通路富集分析发现共30个通路符合阈值要求（P〈0．05），其中32个基因（如ACVR1C、CDH20、THBS1等）及8个生物通路（如Wnt信号通路、P13K—Akt信号通路、TGF-8信号通路等）与癌症的发生发展密切相关。结论OSCC细胞及HOEC均能产生丰富的外泌体。0SCC细胞外泌体基因表达谱与HOEC外泌体基因表达谱相比存在很大的差别，通过对二者基因表达谱的分析，筛选出了可能与口腔鳞癌发生发展相关的差异表达基因及生物通路，为寻找与口腔鳞癌相关的特异性外泌体奠定了基础。

关键词：口腔鳞癌外泌体分离鉴定基因表达谱

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Expressions of the imprinted genes from cluster dill-Dio3 in corticospinal projection neurons

Expressions of the imprinted genes from cluster Dill-Dio3 in...

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中国神经科学学会第九届全国学术会议暨第五次会员代表大会

作者： CS QU,Yj YANG,HP TAO,j QU,jG CHEN~* School of Ophthalmology and Optometry,Wenzhou Medical Collage,the Key Laboratory of Visual Science,Wenzhou, China

＜正＞The corticospinal projection neurons（CSPN）,originated from the layer V of cerebral cortex,generate neural impulses and control execution of movement.Malfunction of CSPN give rise to upper motor neuron（UMN） syndrome.To identify the molecules of the motor neuron related diseases,we labeled the CSPN of postnatal mice by a retrograde tracer Red Beads,and isolated them by laser capture micro-dissection（LCMD）.Started with gene expression screening,we found that maternally expressed gene 3（Meg3） and Meg8 were highly enriched in CSPN during the early development.Meg3 and Meg8 are colocalized with Ctip2,a marker of the layer V.Meg3 and Meg8 are from a transcription unit located in the imprinted cluster dill-Dio3,whereas a paternally expressed gene Rtll is known in the opposite strand.Rtll had a minimal expression in the cortex as determined by in situ hybridization. The homologous genes Meg3 and Meg8 were also expressed in the deep cortical layer in a human brain of 27 week gestation.The different expression pattern between Meg3 and Rtll suggests that the maternally genetic contributions may be important for the early cortical development.Current effect is directed to identify the micro RNAs in dill- Dio3 that inhibit the expression of Rtll.This study may help us to better understand the human disorders due to the maternally deletion of this imprinted cluster.

关键词： CSPN LCMD imprinted gene Meg3 Rtll

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